In order to provide precise guidance for the landing of carrier-based aircrafts, the phased array antenna and the principle of time reference beam scanning are used in the carrier-borne Microwave Landing System (MLS).Ship motion may change the relative position of antenna elements, which will cause the guidance error. In this paper, the models of phased array antenna pattern and antenna vibration error are established, a simulation analysis is made to the effect of phased array antenna's random vibration in three axial directons on the guiding performance of carrier-borne MLS, and a scheme is proposed for suppressing the guidance error of the MLS caused by ship motion. The simulation results show that, the algorithm can stably track the random motion of the ship body, make motion compensation to the phased array antennas of carrier-borne MLS in three dimensions, greatly improve the quality of the received signal, and improve the guidance performance of MLS to a certain extent.